its a 100K mile car. I would anticipate Shocks/Spreings needing replacement. In a year or 2 you are looking at 120K mile service (ie, a 60k mile service) which would mean new waterpump and belts/tensioners etc; brake pads/rotors may also need replacement (they are a very easy DIY repair, btw).
The trans/clutch rebuilds are a plus imho, as long as you see the reciepts.
Rear tires wear out, typically, in the 10-15K mile range depending on use. May want to price check what replacements will run (ie, 17" 18"?)
Some say that if the car has higher miles, it likely won't have IMS (intermediate shaft) or RMS (rear main seal) issues. That they tend to snag the cars that are underdriven. Others will say the opposite. Since porsches like to be driven, I am of the former idea.
"D" chunking of engines has also been reported.
If i was to buy a 996, I would budget, worst case, a fund for a replacement motor (used, "new" your choice).
They are a world apart from your SC. They have modern heat, AC, comfort and convenience items. They are not as "raw" as the SC, but much faster overall. 300hp! for under 20K!
read here too:
http://forums.pelicanparts.com/porsche-marketplace-discussion/509248-market-value-99-00-911-a.html